I am a bioinformatics consultant specializing in omics data and glycobiology with a background in applied science, concentrating in biochemistry and molecular biology.

I am open for projects in bioinformatics and omics data analysis. Reach out and connect via LinkedIn. Link

Throughout my life, I’ve been tinkering with computers and the outdoors, which naturally led me to support the projects I pursue. Past experiences involved developing computational glyco- and proteomics tools that enable the discovery and application of novel phosphopeptides and glycopeptides with desired properties.

I have a Master's degree in Omics Data Analysis from the University of Vic - Central University of Catalonia (UVic-UCC) and I got my Bachelor's degree from University of Wisconsin-Stout in Applied Science - Biochemistry and Molecular Biology. I enjoy exploring and dabbling in the intersection of different omics fields with the aid of computational tools. As for recent projects, I am researching at the University of Valencia on the glycovirology of rotaviruses. The projects listed below highlight some of those adventures.

Here is a list of recent projects I have been toying with on my free time.

1. Glycopeptide Sequence Finder

• A script for hunting (protease-digested) N/O/C-linked glycopeptides in protein/proteome FASTA files based on sequon (motif). It includes a zoo library of digested glycopeptides from various model organisms, common livestock & crops, sea critters and a host of fungus & viral pathogens. Glycopeptide_Sequence_Finder

2. Glycoproteomics Graph Tool

• Neo4j based graph knowledge base for storing glycoproteomics records in context to the central dogma of molecular biology. Glycoproteomics_Graph_Tool

3. Glycopeptide Proteoform Generator

• A script to generate proteoforms by reading glycopeptide data from a CSV file, with limits on the number of proteoforms, saving results in both CSV and text file formats for each protein. Glycopeptide_Proteoform_Generator

4. Cross Species Pathway Analysis Pipeline

• The Cross-Species Pathway Analysis Pipeline is an automated workflow designed to compare enzymatic pathways, such as the N-linked glycosylation pathway, across of species by integrating NCBI Datasets, BLAST+, and standard bioinformatics tools. cross_species_pathway_analysis_pipeline

Here is a list of past projects I have worked on, with links to related GitHub repositories if they are available.

1. Glycopeptide Data Analysis (Final Master Project - UVic)

• Comprehensive analysis of viral glycopeptides, including in-silico sequence prediction, conservation visualization via MSA, and experimental mass spectrometry data analysis. Link

2. Omics Data Analysis Projects (UVic)

• Examples of past omics data analysis projects in genomics, transcriptomics, proteomics, epigenetics, metabolomics, metagenomics, microbiomes and more! Link

3. Glycoproteomics Knowledge Database Development

• Developed a Neo4j graph database for glycomics, integrating public multi-omics data.

4. Glycoproteomics Mass Spectrometry Deep Learning Pipeline (Contributor)

• Optimized a Python-based machine learning pipeline for glycoproteomics mass spectrometry, improving the accuracy of N-glycopeptide identification using deep learning models to analyze fragmentation patterns. Link

5. Dual-Ti-IMAC for Spike Protein Glycopeptide Analysis

• Developed a dual-functional Ti-IMAC method to characterize SARS-CoV-2 Spike protein glycosylation, identifying O-linked and M6P glycoforms. Link

6. O-Linked Glycoproteomics of Alzheimer's Disease Progression

• Monitored changes in the O-glycoproteome in the CSF of patients with progressing stages of AD. LINK

7. N-Linked Glycoform Categorization and Glycopeptide Data Analysis

• Developed R scripts for categorizing glycoforms based on mass spectrometry data, contributing to the analysis of glycosylation patterns in diseases. Link

• Languages: Python, R, Bash
• Data Management: SQL, Neo4j - Cypher
• Data Visualization: R Shiny, Neodash, ggplot2
• Bioinformatics: Omics Data Analysis, Computational Mass Spectrometry, Proteomics, Glycomics, Glycoproteomics

Couple of the starters projects I am working on for LLM agent use in computational biology research.

• TEXT_RAG Link - A RAG that constructs a ChromaDB vector database for LLM querying of PDFs, HTMLs, and TXT files.

• csv_column_text_translator Link - Use LLMs to translate csv text column data to language of choice.

1. In-depth Site-Specific O-Glycosylation Analysis of Glycoproteins and Endogenous Peptides in Cerebrospinal Fluid (CSF) from Healthy Individual, Mild Cognitive Impairment (MCI) and Alzheimer’s disease (AD) patients

   • Z. Chen, Q. Yu, J. Johnson, R. Shipman, X. Zhong, J. Huang, S. Asthana, C. Carlsson, O. Okonkwo, L. Li
   • Published: December 2021

2. Simultaneous Enrichment and Separation of Neutral and Sialyl Glycopeptides of SARS-COV-2 Spike Protein Enabled by Dual-functionalized Ti-IMAC Material

   • J. Huang, W. Danqing, R. Shipman, Z. Zexin, L. Yuan, L. Li
   • Published: June 2021

3. In-depth site-specific analysis of N-glycoproteome in human cerebrospinal fluid (CSF) and glycosylation landscape changes in Alzheimer's disease (AD)

   • Z. Chen, Q. Yu, Q. Yu, J. Johnson, R. Shipman, X. Zhong, J. Huang, S. Asthana, C. Carlsson, O. Okonkwo, L. Li
   • Published: April 2021

4. Activity of Phosvitin in Hydroxyapatite Acid-Damage Immersion and Antimicrobial Assays

   • R. Shipman, S. Doering, J. Hemsath, E.J. Lee, J. E. Grant
   • Published: October 2020

• Mapping the Glycosylation Landscape of the Rotavirus A Spike Protein Domain VP8*

  • R. Shipman, S. López-Navarro, R. Cárcamo-Calvo, R. Gozalbo-Rovira, and J. Rodríguez Díaz
  • 8th Glycobasque Conference, San Sebastian, Spain 2025

• A Property Graph Tool for Glycan Structural Information

  • R. Shipman, K. Islas-Rios, N. Kitagawa, D. Serie, and M. P. Campbell
  • 6th Glycobasque Conference, Bilbao, Spain 2023

• Targeting the Sugar Code: Serum Glycoproteome Profiling for Early Detection of Advanced Adenoma and Colorectal Cancer

  • J. Liu, S. Grupta, A. Shaukat, N.S. Ding, H. Pohl, K. Desai, D. Chandraasekar, C. Guerrier, P. Ramachandran, K. Islas-Rios, R. Shipman, T. Caval, M. Campbell, C. Dhar, G. Xu, F. Schwarz, D. Serie, E. Dekker, M. Wallace, D. Hommes, F. May
  • American College of Gastroenterology ACG 2023

• Accurate Relative Glycoproteomic Quantitation in Complex Matrices (TMT, DDA-LFQ, PRM, and MS1 Filtering) Utilizing High-resolution Liquid Chromatography-Mass Spectrometry

  • G. Gzerwieniec, I. Hundal, A. Antonopolis, R. Cheng, R. Shipman, X. Cong
  • Glyco26 2023

• D-Va: prediction and interpretation of intact N-glycopeptide tandem mass spectra by deep learning

  • Z. Liang, M. P. Campell, R. Shipman, M. Gandhi, P. Aiyetan, N. Kitagawa, D. Serie
  • American Society for Mass Spectrometry 2023

• Evaluating a Glycan Database And Glycopeptide Result Converter Using Human Serum Across Multiple Glycopeptide Search Engines

  • M. Gandhi, R. Shipman, M. P. Campell, N. Kitagawa, Z. Liang, G. Czerwieniec, X. Cong, D. Serie, K. Lindpaintner
  • Society for Glycobiology 2022

• An informatic approach to in-depth site-specific analysis of the glycoproteome in human cerebrospinal fluid and glycosylation alterations in Alzheimer's disease

  • R. Shipman, Z. Chen, Q. Yu, J. Johnson, X. Zhong, J. Huang, S. Asthana, C. Carlsson, O. Okonkwo, L. Li
  • North American Mass Spec Summer School 2020

• Optimization of Protein Extraction and Identification from the European Green Crab

  • N. Wrobel, G. Dachel, R. Shipman, A.D. Myracle, J.E. Grant
  • Experiment Biology 2019 – The American Society for Biochemistry and Molecular Biology

• Modulation of gap junctional intercellular communication in HaCaT cells by xenobiotics

  • R. Shipman, J. Jost, P. Waldmann, D. Pollet
  • Experiment Biology 2019 – The American Society for Biochemistry and Molecular Biology

• In-depth site-specific analysis of glycoproteome in human cerebrospinal fluid (CSF) and glycosylation alterations in Alzheimer’s disease (AD)

  • Z. Chen, Q. Yu, J. Johnson, R. Shipman, X. Zhong, J. Huang, S. Asthana, C. Carlsson, O. Okonkwo, L. Li
  • American Society for Mass Spectrometry 2018

• Development of an Immersion Model for Tooth Decay Observed via Scanning Electron Microscopy, Atomic Force Microscopy and Flame Atomic Absorption Spectroscopy

  • R. Shipman, B. Quelle, J. Grant, E.J. Lee
  • Experiment Biology 2018 – The American Society for Biochemistry and Molecular Biology

• In-depth site-specific analysis of glycoproteins and endogenous peptides in cerebrospinal fluid (CSF) from healthy individual, mild cognitive impairment (MCI) and Alzheimer’s disease (AD) patients

  • Z. Chen, Q. Yu, J. Johnson, R. Shipman, X. Zhong, J. Huang, S. Asthana, C. Carlsson, O. Okonkwo, L. Li
  • Wisconsin Alzheimer’s Disease & Related Disorders Research Day 2018

• Effect of Metal Binding Proteins on the Surface of a Model of Tooth Decay

  • R. Shipman, J. Grant, E. J. Lee
  • Research in the Rotunda 2018 – University of Wisconsin System

• Assessing Student Competencies Using Rubrics Associated with Figure Legends and Ability to Perform the Bradford Assay in a 400-Level Undergraduate Proteomics Course

  • J. Grant, R. Shipman
  • Experiment Biology 2017 – The American Society for Biochemistry and Molecular Biology

• Effects of Phosvitin on Intestinal Epithelial Cell Viability Analyzed by Flow Cytometry and AlamarBlue Cell Viability Assay

  • R. Shipman, J. Talukder
  • Experiment Biology 2017 – The American Society for Biochemistry and molecular Biology